Variant report

Variant	rs11853377
Chromosome Location	chr15:41244166-41244167
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:41244087-41246309	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr15:41244084-41244183	K562	blood:	n/a	n/a
3	HCFC1	chr15:41243714-41246867	Hela-S3	cervix:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:41243575..41247241-chr15:41275161..41277167,3	MCF-7	breast:
2	chr15:41219948..41223850-chr15:41241031..41249080,13	K562	blood:
3	chr15:41196932..41200984-chr15:41244050..41248455,6	K562	blood:
4	chr15:41046641..41048842-chr15:41243931..41246219,2	K562	blood:
5	chr15:41219573..41224863-chr15:41243808..41249661,11	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CHAC1-1	chr15:41244055-41244195	XLOC_011224
2	lnc-INO80-2	chr15:41243982-41244186	NONHSAT041901

No data

Variant related genes	Relation type
CHAC1	TF binding region
ISCA1P4	TF binding region
ENSG00000137824	Chromatin interaction
ENSG00000251161	Chromatin interaction
ENSG00000128917	Chromatin interaction
ENSG00000128908	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10851400	0.98[ASN][1000 genomes]
rs11070313	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11070314	0.94[ASN][1000 genomes]
rs11557249	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11634736	0.92[EUR][1000 genomes]
rs11854054	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11857572	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12593739	0.90[ASN][1000 genomes]
rs28575174	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924520	0.93[ASN][1000 genomes]
rs60588038	0.94[ASN][1000 genomes]
rs7174555	0.91[ASN][1000 genomes]
rs7175269	0.91[EUR][1000 genomes]
rs745299	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8042127	0.84[ASN][1000 genomes]
rs8042230	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904101	chr15:40979651-41275014	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	esv1819092	chr15:41017682-41255750	Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
3	nsv904103	chr15:41123172-41275014	Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv904105	chr15:41149824-41275014	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
5	nsv904106	chr15:41221067-41259523	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11853377	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41235400-41244600	Weak transcription	NHLF	lung
2	chr15:41235800-41244800	Weak transcription	Esophagus	oesophagus
3	chr15:41236200-41244600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr15:41238600-41244400	Weak transcription	GM12878-XiMat	blood
5	chr15:41241200-41244200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr15:41241400-41244400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr15:41241400-41244600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr15:41241600-41244400	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr15:41241600-41244400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr15:41241800-41244400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr15:41241800-41244600	Weak transcription	Primary hematopoietic stem cells	blood
12	chr15:41241800-41244600	Weak transcription	Fetal Thymus	thymus
13	chr15:41241800-41244600	Weak transcription	Gastric	stomach
14	chr15:41242000-41244200	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr15:41242000-41244400	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr15:41242000-41244400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr15:41242000-41244400	Weak transcription	Colonic Mucosa	Colon
18	chr15:41242000-41244400	Weak transcription	Pancreas	Pancrea
19	chr15:41242000-41244400	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr15:41242000-41244600	Weak transcription	Left Ventricle	heart
21	chr15:41242200-41244400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr15:41242200-41244400	Weak transcription	Lung	lung
23	chr15:41242200-41244400	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr15:41242200-41244600	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr15:41242200-41244600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr15:41242400-41244200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr15:41242400-41244200	Weak transcription	NHEK	skin
28	chr15:41242400-41244400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr15:41242400-41244400	Weak transcription	Duodenum Mucosa	Duodenum
30	chr15:41242400-41244400	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr15:41242400-41244600	Weak transcription	Adipose Nuclei	Adipose
32	chr15:41242400-41244600	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr15:41242400-41244800	Weak transcription	Psoas Muscle	Psoas
34	chr15:41242600-41244400	Weak transcription	Fetal Intestine Small	intestine
35	chr15:41242600-41244400	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr15:41242600-41244400	Weak transcription	K562	blood
37	chr15:41242600-41244600	Weak transcription	Fetal Intestine Large	intestine
38	chr15:41243000-41244400	Weak transcription	Liver	Liver
39	chr15:41243800-41244400	Enhancers	Hela-S3	cervix
40	chr15:41244000-41244200	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
41	chr15:41244000-41244400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
42	chr15:41244000-41244400	Active TSS	Stomach Mucosa	stomach
43	chr15:41244000-41244400	Enhancers	Dnd41	blood
44	chr15:41244000-41244600	Enhancers	Primary T killer memory cells from peripheral blood	blood
45	chr15:41244000-41245200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin

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